Analysis of the algorithm: From embeddings to prioritized genes.

The algorithm transformed the similarity matrix to make it compatible with the embedding process. Once this was done for each network and embedding type, it was integrated by embedding type. Below there is a general analysis of the properties of each matrix in the different phases of the process, including the graph building process for each layer.

Annotations Properties

Table 1. Annotation descriptors.

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2294 2.261042369703787 23.27548667222241
hippie_ppi 1 2985 84.68724915097252 150.1286010250888
pathway 1 479 6.75436035343834 16.179001796162975
string_ppi 1 7338 610.0699285559645 500.6662722348227

Individual Processing Graph steps

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Embedding Process

Table 2. Uncombined Embedding Matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_pearson ct 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson el 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_pearson raw_sim 17354x17354 301161316 106761316 0.35449876968926514
DepMap_effect_pearson rf 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ct 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman el 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ka 17354x17354 301161316 194719108 0.6465608219084817
DepMap_effect_spearman raw_sim 17354x17354 301161316 194701754 0.6465031983058541
DepMap_effect_spearman rf 17354x17354 301161316 301161316 1.0
gene_PS ct 362x362 131044 112096 0.8554073440981655
gene_PS el 362x362 131044 7680 0.05860626964988859
gene_PS ka 362x362 131044 2028 0.015475718079423705
gene_PS node2vec 362x362 131044 131044 1.0
gene_PS raw_sim 362x362 131044 1666 0.012713287140197186
gene_PS rf 362x362 131044 7680 0.05860626964988859
gene_TF ct 3871x3871 14984641 14984637 0.9999997330600046
gene_TF el 3871x3871 14984641 14969165 0.9989672091576969
gene_TF ka 3871x3871 14984641 5275373 0.35205201112258877
gene_TF raw_sim 3871x3871 14984641 5271502 0.35179367994201527
gene_TF rf 3871x3871 14984641 14969165 0.9989672091576969
hippie_ppi ct 15763x15763 248472169 248472169 1.0
hippie_ppi el 15763x15763 248472169 245768483 0.9891187571997249
hippie_ppi ka 15763x15763 248472169 421467 0.0016962342370022132
hippie_ppi node2vec 15763x15763 248472169 248472169 1.0
hippie_ppi raw_sim 15763x15763 248472169 408340 0.0016434033704595704
hippie_ppi rf 15763x15763 248472169 245768483 0.9891187571997249
pathway ct 5611x5611 31483321 31482925 0.9999874219114305
pathway el 5611x5611 31483321 25851467 0.8211162666098663
pathway ka 5611x5611 31483321 362997 0.011529819233491919
pathway node2vec 5611x5611 31483321 31483321 1.0
pathway raw_sim 5611x5611 31483321 357386 0.011351597882574078
pathway rf 5611x5611 31483321 25851467 0.8211162666098663
string_ppi ct 16111x16111 259564321 259564321 1.0
string_ppi el 16111x16111 259564321 252333871 0.9721438987756719
string_ppi ka 16111x16111 259564321 497009 0.0019147816544478006
string_ppi node2vec 16111x16111 259564321 259564321 1.0
string_ppi raw_sim 16111x16111 259564321 480917 0.001852785460448549
string_ppi rf 16111x16111 259564321 252333871 0.9721438987756719

Table 3. Integrated Embedding Matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 29867x29867 892037689 779232361 0.8735419709379566
integration_mean_by_presence el 29867x29867 892037689 544165899 0.6100256813252203
integration_mean_by_presence ka 29867x29867 892037689 149003403 0.16703711607413932
integration_mean_by_presence node2vec 18083x18083 326994889 315076927 0.9635530633630179
integration_mean_by_presence rf 29867x29867 892037689 544165899 0.6100256813252203
mean ct 29867x29867 892037689 779232361 0.8735419709379566
mean el 29867x29867 892037689 544165899 0.6100256813252203
mean ka 29867x29867 892037689 149003403 0.16703711607413932
mean node2vec 18083x18083 326994889 315076927 0.9635530633630179
mean rf 29867x29867 892037689 544165899 0.6100256813252203

Weight values